*/
#include "gmxpre.h"
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
+
+#include <algorithm>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-typedef struct
-{
- char sanm[12];
- int natm;
- int nw;
- char anm[6][12];
-} t_simat;
-
-typedef struct
-{
- char reso[12];
- char resn[12];
- int nsatm;
- t_simat sat[3];
-} t_simlist;
real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
{
return tmass;
}
-real calc_geom(int isize, atom_id *index, rvec *x, rvec geom_center, rvec min,
- rvec max, gmx_bool bDiam)
+real calc_geom(int isize, atom_id *index, rvec *x, rvec geom_center, rvec minval,
+ rvec maxval, gmx_bool bDiam)
{
real diam2, d;
- char *grpnames;
int ii, i, j;
clear_rvec(geom_center);
diam2 = 0;
if (isize == 0)
{
- clear_rvec(min);
- clear_rvec(max);
+ clear_rvec(minval);
+ clear_rvec(maxval);
}
else
{
}
for (j = 0; j < DIM; j++)
{
- min[j] = max[j] = x[ii][j];
+ minval[j] = maxval[j] = x[ii][j];
}
for (i = 0; i < isize; i++)
{
rvec_inc(geom_center, x[ii]);
for (j = 0; j < DIM; j++)
{
- if (x[ii][j] < min[j])
+ if (x[ii][j] < minval[j])
{
- min[j] = x[ii][j];
+ minval[j] = x[ii][j];
}
- if (x[ii][j] > max[j])
+ if (x[ii][j] > maxval[j])
{
- max[j] = x[ii][j];
+ maxval[j] = x[ii][j];
}
}
if (bDiam)
for (j = i + 1; j < isize; j++)
{
d = distance2(x[ii], x[index[j]]);
- diam2 = max(d, diam2);
+ diam2 = std::max(d, diam2);
}
}
else
for (j = i + 1; j < isize; j++)
{
d = distance2(x[i], x[j]);
- diam2 = max(d, diam2);
+ diam2 = std::max(d, diam2);
}
}
}
svmul(1.0 / isize, geom_center, geom_center);
}
- return sqrt(diam2);
+ return std::sqrt(diam2);
}
void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
double *bfac, int *bfac_nr, gmx_bool peratom)
{
- FILE *out;
real bfac_min, bfac_max;
int i, n;
gmx_bool found;
bfac_max /= 10;
bfac_min /= 10;
}
- while ((fabs(bfac_max) < 0.5) && (fabs(bfac_min) < 0.5))
+ while ((std::abs(bfac_max) < 0.5) && (std::abs(bfac_min) < 0.5))
{
fprintf(stderr,
"Range of values for B-factors too small (min %g, max %g) "
zmin = 1e10;
for (i = 0; (i < natoms); i++)
{
- xmin = min(xmin, x[i][XX]);
- ymin = min(ymin, x[i][YY]);
- zmin = min(zmin, x[i][ZZ]);
- bfac_min = min(bfac_min, atoms->pdbinfo[i].bfac);
- bfac_max = max(bfac_max, atoms->pdbinfo[i].bfac);
+ xmin = std::min(xmin, x[i][XX]);
+ ymin = std::min(ymin, x[i][YY]);
+ zmin = std::min(zmin, x[i][ZZ]);
+ bfac_min = std::min(bfac_min, atoms->pdbinfo[i].bfac);
+ bfac_max = std::max(bfac_max, atoms->pdbinfo[i].bfac);
}
fprintf(stderr, "B-factors range from %g to %g\n", bfac_min, bfac_max);
for (i = 1; (i < 12); i++)
a0++;
r0++;
- nx = (int) (gridsize[XX] + 0.5);
- ny = (int) (gridsize[YY] + 0.5);
- nz = (int) (gridsize[ZZ] + 0.5);
+ nx = static_cast<int>(gridsize[XX] + 0.5);
+ ny = static_cast<int>(gridsize[YY] + 0.5);
+ nz = static_cast<int>(gridsize[ZZ] + 0.5);
nbox = nx * ny * nz;
if (TRICLINIC(box))
{
}
for (i = 0; i < 24; i += 2)
{
- fprintf(out, "CONECT%5d%5d\n", a0 + rectedge[i], a0 + rectedge[i
- + 1]);
+ fprintf(out, "CONECT%5d%5d\n", a0 + rectedge[i], a0 + rectedge[i + 1]);
}
}
}
real ux, uy, uz, costheta, sintheta;
costheta = cos_angle(principal_axis, targetvec);
- sintheta = sqrt(1.0-costheta*costheta); /* sign is always positive since 0<theta<pi */
+ sintheta = s
td::sqrt(1.0-costheta*costheta); /* sign is always positive since 0<theta<pi */
/* Determine rotation from cross product with target vector */
cprod(principal_axis, targetvec, rotvec);
"For complex molecules, the periodicity removal routine may break down, "
"in that case you can use [gmx-trjconv]."
};
- static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
+ static real dist = 0.0;
static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
FALSE, bCONECT = FALSE;
static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
t_topology *top = NULL;
t_atoms atoms;
char *grpname, *sgrpname, *agrpname;
- int isize, ssize, tsize, asize;
- atom_id *index, *sindex, *tindex, *aindex;
- rvec *x, *v, gc, min, max, size;
+ int isize, ssize, asize;
+ atom_id *index, *sindex, *aindex;
+ rvec *x, *v, gc, rmin, rmax, size;
int ePBC;
matrix box, rotmatrix, trans;
rvec princd, tmpvec;
- gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
+ gmx_bool bIndex, bSetSize, bSetAng, bDist, bSetCenter, bAlign;
gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
- real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
+ real diam = 0, mass = 0, d, vdw;
gmx_atomprop_t aps;
gmx_conect conect;
output_env_t oenv;
}
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
- bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';
+
+ GMX_RELEASE_ASSERT(btype[0] != NULL, "Option setting inconsistency; btype[0] is NULL");
+
+ bCalcDiam = (btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o');
infile = ftp2fn(efSTX, NFILE, fnm);
if (bMead)
{
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
- vol, 100*((int)(vol*4.5)));
+ vol, 100*(static_cast<int>(vol*4.5)));
}
if (bMead || bGrasp || bCONECT)
{
sig6 = c12/c6;
}
- vdw = 0.5*pow(sig6, 1.0/6.0);
+ vdw = 0.5*std::pow(sig6, static_cast<real>(1.0/6.0));
}
else
{
ssize = atoms.nr;
sindex = NULL;
}
- diam = calc_geom(ssize, sindex, x, gc, min, max, bCalcDiam);
- rvec_sub(max, min, size);
+ diam = calc_geom(ssize, sindex, x, gc, rmin, rmax, bCalcDiam);
+ rvec_sub(rmax, rmin, size);
printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*acos(cos_angle_no_table(box[YY], box[ZZ])),
+ RAD2DEG*std::acos(cos_angle_no_table(box[YY], box[ZZ])),
norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*acos(cos_angle_no_table(box[XX], box[ZZ])),
+ RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[ZZ])),
norm2(box[YY]) == 0 ? 0 :
- RAD2DEG*acos(cos_angle_no_table(box[XX], box[YY])));
+ RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[YY])));
printf(" box volume :%7.2f (nm^3)\n", det(box));
}
"zero mass (%g) or volume (%g)\n", mass, vol);
}
- scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho, 1.0/3.0);
+ scale[XX] = scale[YY] = scale[ZZ] = std::pow(dens/rho, static_cast<real>(1.0/3.0));
fprintf(stderr, "Scaling all box vectors by %g\n", scale[XX]);
}
scale_conf(atoms.nr, x, box, scale);
if (bCalcGeom)
{
/* recalc geometrical center and max and min coordinates and size */
- calc_geom(ssize, sindex, x, gc, min, max, FALSE);
- rvec_sub(max, min, size);
+ calc_geom(ssize, sindex, x, gc, rmin, rmax, FALSE);
+ rvec_sub(rmax, rmin, size);
if (bScale || bOrient || bRotate)
{
printf("new system size : %6.3f %6.3f %6.3f\n",
}
}
- if (bSetSize || bDist || (btype[0][0] == 't' && bSetAng))
+ if ((btype[0] != NULL) && (bSetSize || bDist || (btype[0][0] == 't' && bSetAng)))
{
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
- box[ZZ][ZZ] = d*sqrt(2)/2;
+ box[ZZ][ZZ] = d*std::sqrt(2.0)/2.0;
}
else
{
box[XX][XX] = d;
box[YY][XX] = d/3;
- box[YY][YY] = d*sqrt(2)*2/3;
+ box[YY][YY] = d*std::sqrt(2.0)*2.0/3.0;
box[ZZ][XX] = -d/3;
- box[ZZ][YY] = d*sqrt(2)/3;
- box[ZZ][ZZ] = d*sqrt(6)/3;
+ box[ZZ][YY] = d*std::sqrt(2.0)/3.0;
+ box[ZZ][ZZ] = d*std::sqrt(6.0)/3.0;
}
break;
}
/* print some */
if (bCalcGeom)
{
- calc_geom(ssize, sindex, x, gc, min, max, FALSE);
+ calc_geom(ssize, sindex, x, gc, rmin, rmax, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
}
if (bOrient || bScale || bDist || bSetSize)
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*acos(cos_angle_no_table(box[YY], box[ZZ])),
+ RAD2DEG*std::acos(cos_angle_no_table(box[YY], box[ZZ])),
norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*acos(cos_angle_no_table(box[XX], box[ZZ])),
+ RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[ZZ])),
norm2(box[YY]) == 0 ? 0 :
- RAD2DEG*acos(cos_angle_no_table(box[XX], box[YY])));
+ RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[YY])));
printf("new box volume :%7.2f (nm^3)\n", det(box));
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff